Hi,
there’s no direct connection between those two modules.
Are the relays disconnected or connected to some load?
Is to the Channel A connected any sensor?
How do you power the Core Module?
Inductive loads can create false pulses. What happens if you disconnect the solenoid, or sensor (do you use that flow sensor?). That hall flow sensor can react to magnetic field from solenoids.
The solution (in case the issue is the switched noise) might be to use stronger pull-up. Instead of internal pullup you can use external pullup with lower resistance which is on the Sensor Module. Or add external one.